Oct2007 ontology report

Ontology Development & GO Editorial Office Report - September 2007

I. Ontology Development

• SourceForge
  • Items opened: 52
  • Items closed: 67
    • GO Eds: 36
    • MOD curators: 4 (details in Appendix 1)
    • GO Ed/MOD collaborations: 27 (details in Appendix 2)
  • Items still open: 254
    • assigned, GO Eds: 38
    • assigned, MOD curators: 52
    • unassigned: 164

• Cardiovascular physiology & Muscle development: Changes have gone live. Details on wiki:
  • http://gocwiki.geneontology.org/index.php/Cardiovascular_physiology/develoment
  • http://wiki.geneontology.org/index.php/Muscle_Development).
• Other content items resolved
  • Another big load of synonyms for enzyme activity terms added, derived from EC via IntEnz (Midori, Colin Batchelor)
  • Terms added for PAMGO (http://gocwiki.geneontology.org/index.php/PAMGO_2007)
  • PIR GO slim added
  • Various small things for SourceForge items

• Other content items in progress
  • Content meeting on lung development to be held in December (http://wiki.geneontology.org/index.php/Lung_Development)
  • Just resuming work on the remaining sensu terms; fruiting body terms resolved (http://gocwiki.geneontology.org/index.php/Meeting_Notes_3)
  • David and Tanya (and other curators, as need arises) are sorting out the regulation problems originally identified in Chris' file of "regulation of non-process" anomalies (details at http://gocwiki.geneontology.org/index.php/Regulation_Main_Page, especially http://gocwiki.geneontology.org/index.php/Part_3)
  • Gearing up to return attention to links between function and process (Skype/Webex session Oct. 31; info on wiki at http://gocwiki.geneontology.org/index.php/Function-Process_Links)
  • Additional enzyme activity terms in function, for EC entries not yet represented in GO (Midori, Colin Batchelor)
  • Various SourceForge items

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• Jane still on maternity leave
• Amelia visiting Berkeley database/software group

• OBO-Edit working group:
  • Additional OBO-Edit 2.0 betas released and tested, including new search/filtering interface

• Advocacy/outreach group (Jane; Jen while Jane is away):
  • Annotation: Grape (Vitis vinifera) genome to be annotated by Franco-Italian consortium, headed by Giorgio Valle and Erika Feltrin.
  • November 2007 newsletter in progress
  • Usual gohelp traffic

• Conferences/meetings
  • Preparation for workshop on "Applied GO", Nov. 7-9, Bari, Italy (Midori)

• Anything else
  • NAR database issue manuscript accepted
  • Scripts for various curator tasks (Jen)
  • GO bibliography has 1642 entries

Appendix 1: MOD curators' SF items
1669585 Rama, Rob, Val
1803319 David
1803383 David
1809814 David, Doug

Appendix 2: GO Ed-MOD collaboration SF items - MOD curator(s) involved
852977 David, Kimberly
899726 TAIR curators
966600 Pankaj, Tanya
1100957 David, Sue
1237306 Rama, Rob, Val, Simon
1337453 Rama, Val
1397633 TAIR curators
1465845 David, Doug
1572258 Alex
1600457 Alex
1619099 Donghui, Tanya
1653166 Tanya
1666307 Val, Maria, transport group
1698959 Pascale
1708056 Ben
1740359 Alex
1757511 Val
1787598 Val, David
1803653 Doug, ZFIN curators
1805582 Alex, Ev
1806426 Val
1808234 Karen C
1808267 Val, Stacia
1810389 Michelle
1811390 Rama, Val
1812218 Alex
1814623 Eurie

(Note: "MOD curator" is shorthand for any non-GO-Ed curator)

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